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Kobresia species are common in meadows on the Qinghai–Tibet Plateau. They are important food resources for local livestock, and serve a critical foundation for ecosystem integration. Genetic resources of Kobresia species are scarce. Here, we generated a chromosome-level genome assembly for K. myosuroides (Cyperaceae), using PacBio long-reads, Illumina short-reads, and Hi–C technology. The final assembly had a total size of 399.9 Mb with a contig N50 value of 11.9 Mb. The Hi–C result supported a 29 pseudomolecules model which was in consistent with cytological results. A total of 185.5 Mb (44.89% of the genome) transposable elements were detected, and 26,748 protein-coding genes were predicted. Comparative analysis revealed that Kobresia plants have experienced recent diversification events during the late Miocene to Pliocene. Karyotypes analysis indicated that the fission and fusion of chromosomes have been a major driver of speciation, which complied with the lack of whole-genome duplication (WGD) in K. myosuroides genome. Generally, this high-quality reference genome provides insights into the evolution of alpine sedges, and may be helpful to endemic forage improvement and alpine ecosystem preservation. [ABSTRACT FROM AUTHOR]

Taxol is currently a valuable anticancer drug; however, the accumulated mixture of taxoids can vary greatly among Taxus species. So far, there is very little genomic information for the genus Taxus, except for Taxus baccata. Transcriptome analysis is a powerful approach to explore the different regulatory mechanisms underlying the taxoid biosynthesis pathway in Taxus species. First, we quantified the variation in the taxoid contents between Taxus media and Taxus mairei. The contents of paclitaxel and 10- deacetylpaclitaxel in T. media are higher than that in T. mairei. Then, the transcriptome profiles of T. media and T. mairei were analyzed to investigate the altered expressions. A total of 20,704 significantly differentially expressed genes (DEGs), including 9865 unigenes predominantly expressed in T. media and 10,839 unigenes predominantly expressed in T. mairei, were identified. In total, 120 jasmonic acid-related DEGs were analyzed, suggesting variations in 'response to JA stimulus' and 'JA biosynthetic process' pathways between T. media and T. mairei. Furthermore, a number of genes related to the precursor supply, taxane skeleton formation and hydroxylation, and C13-side chain assembly were also identified. The differential expression of the candidate genes involved in taxoid biosynthetic pathways may explain the variation in the taxoid contents between T. media and T. mairei. [ABSTRACT FROM AUTHOR]

We study the galaxy clustering dependence on the [O II] emission line luminosity in the SDSS DR7 Main galaxy sample at mean redshift z ∼ 0.1. We select volume-limited samples of galaxies with different [O II] luminosity thresholds and measure their projected, monopole and quadrupole two-point correlation functions. We model these observations using the 1 h-1 Gpc Multi Dark-Planck cosmological simulation and generate light cones with the SUrvey Gener A to R algorithm. To interpret our results, we adopt a modified (Sub)Halo Abundance Matching scheme, accounting for the stellar mass incompleteness of the emission line galaxies. The satellite fraction constitutes an extra parameter in this model and allows to optimize the clustering fit on both small and intermediate scales (i.e. rp ≲ 30 h-1 Mpc), with no need of any velocity bias correction. We find that, in the local Universe, the [O II] luminosity correlateswith all the clustering statistics explored and with the galaxy bias. This latter quantity correlates more strongly with the SDSS r-band magnitude than [O II] luminosity. In conclusion, we propose a straightforward method to produce reliable clustering models, entirely built on the simulation products, which provides robust predictions of the typical ELG host halo masses and satellite fraction values. The SDSS galaxy data, MultiDark mock catalogues and clustering results are made publicly available. [ABSTRACT FROM AUTHOR]

Taxus species are well-known for paclitaxel, which exhibits antitumor activities and is used for treating various cancers. Although most Taxus species are widespread in many areas, few studies have characterized the variation in metabolism among different Taxus species. Using an integrated approach involving 'tandem mass tag' labeling and liquid chromatography-tandem mass spectrometry (HPLC-MS), proteomes of T. media and T. mairei were investigated and 4078 proteins were quantified. Screening and classification of differentially expressed proteins revealed many metabolism-associated proteins. In detail, four enzymes involved in the flavonoid biosynthesis pathway were predominantly expressed in T. mairei. Four enzymes associated with supplying precursors for paclitaxel biosynthesis and three cytochrome P450 taxoid oxygenases were preferentially expressed in T. media compared with T. mairei. Furthermore, variations in taxoid contents between T. media and T. mairei were determined using HPLC-MS analysis. Variations in flavonoid contents between T. media and T. mairei were determined by HPLC analysis. A number of differentially expressed proteins may provide an explanation for the variation in metabolisms of different Taxus species. [ABSTRACT FROM AUTHOR]

We have developed an analytical method based on forward-modelling techniques to characterize the high-mass end of the red sequence (RS) galaxy population at redshift z ~ 0.55, from the DR10 BOSS (Baryon Oscillation Spectroscopic Survey) CMASS spectroscopic sample, which comprises ~600 000 galaxies. The method, which follows an unbinned maximum likelihood approach, allows the deconvolution of the intrinsic CMASS colour-colour-magnitude distributions from photometric errors and selection effects. This procedure requires modelling the covariance matrix for the i-band magnitude, g - r colour and r - i colour using Stripe 82 multi-epoch data. Our results indicate that the error-deconvolved intrinsic RS distribution is consistent, within the photometric uncertainties, with a single point (<0.05 mag) in the colour-colour plane at fixed magnitude, for a narrow redshift slice. We have computed the high-mass end (0.55Mi≲ -22) of the 0.55i-band RS luminosity function (RS LF) in several redshift slices within the redshift range 0.52 < z < 0.63. In this narrow redshift range, the evolution of the RS LF is consistent, within the uncertainties in the modelling, with a passively evolving model with Φ* = (7.248 ± 0.204) × 10-4 Mpc-3 mag-1, fading at a rate of 1.5 ± 0.4 mag per unit redshift. We report RS completeness as a function of magnitude and redshift in the CMASS sample, which will facilitate a variety of galaxy-evolution and clustering studies using BOSS. Our forward-modelling method lays the foundations for future studies using other dark-energy surveys like the Extended Baryon Oscillation Spectroscopic Survey or the Dark Energy Spectroscopic Instrument, which are affected by the same type of photometric blurring/selection effects. [ABSTRACT FROM AUTHOR]

Faint red galaxies in the Sloan Digital Sky Survey show a puzzling clustering pattern in previous measurements. In the two-point correlation function (2PCF), they appear to be strongly clustered on small scales, indicating a tendency to reside in massive haloes as satellite galaxies. However, their weak clustering on large scales suggests that they are more likely to be found in low-mass haloes. The interpretation of the clustering pattern suffers from the large sample variance in the 2PCF measurements, given the small volume of the volumelimited sample of such faint galaxies. We present improved clustering measurements of faint galaxies by making a full use of a flux-limited sample to obtain volume-limited measurements with an increased effective volume. In the improved 2PCF measurements, the fractional uncertainties on large scales drop by more than 40 per cent, and the strong contrast between small-scale and large-scale clustering amplitudes seen in previous work is no longer prominent. From halo occupation distribution modelling of the measurements, we find that a considerable fraction of faint red galaxies to be satellites in massive haloes, a scenario supported by the strong covariance of small-scale 2PCF measurements and the relative spatial distribution of faint red galaxies and luminous galaxies. However, the satellite fraction is found to be degenerate with the slope of the distribution profile of satellites in inner haloes. We compare the modelling results with semi-analytic model predictions and discuss the implications. [ABSTRACT FROM AUTHOR]

We present a study of the clustering and halo occupation distribution of Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxies in the redshift range 0.43 < z < 0.7 drawn from the Final SDSS-III Data Release. We compare the BOSS results with the predictions of a halo abundance matching (HAM) clustering model that assigns galaxies to dark matter haloes selected from the large Big Multi Dark N-body simulation of a flat Λ cold dark matter Planck cosmology. We compare the observational data with the simulated ones on a light cone constructed from 20 subsequent outputs of the simulation. Observational effects such as incompleteness, geometry, veto masks and fibre collisions are included in the model, which reproduces within 1σ errors the observed monopole of the two-point correlation function at all relevant scales: from the smallest scales, 0.5 h-1 Mpc, up to scales beyond the baryon acoustic oscillation feature. This model also agrees remarkably well with the BOSS galaxy power spectrum (up to k ~ 1 h Mpc-1), and the three-point correlation function. The quadrupole of the correlation function presents some tensions with observations. We discuss possible causes that can explain this disagreement, including target selection effects. Overall, the standard HAM model describes remarkably well the clustering statistics of the CMASS sample. We compare the stellar-to-halo mass relation for the CMASS sample measured using weak lensing in the Canada--France--Hawaii Telescope Stripe 82 Survey with the prediction of our clustering model, and find a good agreement within 1σ. The BigMD-BOSS light cone including properties of BOSS galaxies and halo properties is made publicly available. [ABSTRACT FROM AUTHOR]

We model the luminosity-dependent projected and redshift-space two-point correlation functions (2PCFs) of the Sloan Digital Sky Survey (SDSS) Data Release 7 Main galaxy sample, using the halo occupation distribution (HOD) model and the subhalo abundance matching (SHAM) model and its extension. All the models are built on the same high-resolution Nbody simulations. We find that the HOD model generally provides the best performance in reproducing the clustering measurements in both projected and redshift spaces. The SHAM model with the same halo-galaxy relation for central and satellite galaxies (or distinct haloes and subhaloes), when including scatters, has a best-fitting X2 around 2-3. We therefore extend the SHAM model to the subhalo clustering and abundance matching (SCAM) by allowing the central and satellite galaxies to have different galaxy-halo relations. We infer the corresponding halo/subhalo parameters by jointly fitting the galaxy 2PCFs and abundances and consider subhaloes selected based on three properties, the mass Macc at the time of accretion, the maximum circular velocity Vacc at the time of accretion, and the peak maximum circular velocity Vpeak over the history of the subhaloes. The three subhalo models work well for luminous galaxy samples (with luminosity above L*). For low-luminosity samples, the Vacc model stands out in reproducing the data, with the Vpeak model slightly worse, while the Macc model fails to fit the data. We discuss the implications of the modelling results. [ABSTRACT FROM AUTHOR]

Several phytohormones have been demonstrated to be involved in iron (Fe) homeostasis. We took advantage of a salicylic acid (SA) biosynthesis defective mutant phytoalexin deficient 4 (pad4: T-DNA Salk_089936) to explore the possible effects of endogenous SA on the morphological and physiological responses to Fe deprivation. The morphological and physiological analysis was carried out between Col-0 and the pad4 mutant. Under an Fe-deficiency treatment, Col-0 showed more severe leaf chlorosis and root growth inhibition compared with the pad4 mutant. The soluble Fe concentrations were significantly higher in pad4 than in Col-0 under the Fe-deficiency treatment. Fe deficiency significantly induced SA accumulation in Col-0 and the loss-of-function of PAD4 blocked this process. The requirement of endogenous SA accumulation for Fe-deficiency responses was confirmed using a series of SA biosynthetic mutants and transgenic lines. Furthermore, a comparative RNA sequencing analysis of the whole seedling transcriptomes between Col-0 and the pad4 mutant was also performed. Based on the transcriptome data, the expression levels of many auxin- and ethylene-response genes were altered in pad4 compared with Col-0. Fe deficiency increases SA contents which elevates auxin and ethylene signalling, thereby activating Fe translocation via the bHLH38/39-mediated transcriptional regulation of downstream Fe genes. [ABSTRACT FROM AUTHOR]

Small- and intermediate-scale galaxy clustering can be used to establish the galaxy-halo connection to study galaxy formation and evolution and to tighten constraints on cosmological parameters. With the increasing precision of galaxy clustering measurements from ongoing and forthcoming large galaxy surveys, accurate models are required to interpret the data and extract relevant information. We introduce a method based on high-resolution N-body simulations to accurately and efficiently model the galaxy two-point correlation functions (2PCFs) in projected and redshift spaces. The basic idea is to tabulate all information of haloes in the simulations necessary for computing the galaxy 2PCFs within the framework of halo occupation distribution or conditional luminosity function. It is equivalent to populating galaxies to dark matter haloes and using the mock 2PCF measurements as the model predictions. Besides the accurate 2PCF calculations, the method is also fast and therefore enables an efficient exploration of the parameter space. As an example of the method, we decompose the redshiftspace galaxy 2PCF into different components based on the type of galaxy pairs and show the redshift-space distortion effect in each component. The generalizations and limitations of the method are discussed. [ABSTRACT FROM AUTHOR]

We reproduce the galaxy clustering catalogue from the SDSS-III Baryon Oscillation Spectroscopic Survey Final Data Release (BOSS DR11&DR12) with high fidelity on all relevant scales in order to allow a robust analysis of baryon acoustic oscillations and redshift space distortions. We have generated (6000) 12 288 MultiDark PATCHY BOSS (DR11) DR12 light cones corresponding to an effective volume of ∼192 000 [h-1 Gpc]³ (the largest ever simulated volume), including cosmic evolution in the redshift range from 0.15 to 0.75. The mocks have been calibrated using a reference galaxy catalogue based on the halo abundance matching modelling of the BOSS DR11&DR12 galaxy clustering data and on the data themselves. The production follows three steps. First, we apply the PATCHY code to generate a dark matter field and an object distribution including non-linear stochastic galaxy bias. Secondly, we run the halo/stellar distribution reconstruction HADRON code to assign masses to the various objects. This step uses the mass distribution as a function of local density and non-local indicators (i.e. tidal field tensor eigenvalues and relative halo exclusion separation for massive objects) from the reference simulation applied to the corresponding patchy dark matter and galaxy distribution. Finally, we apply the SUGAR code to build the light cones. The resulting MultiDarkPATCHY mock light cones reproduce the number density, selection function, survey geometry, and in general within 1s, for arbitrary stellar mass bins, the power spectrum up to k = 0.3 h Mpc-1, the two-point correlation functions down to a few Mpc scales, and the three-point statistics of the BOSS DR11&DR12 galaxy samples. [ABSTRACT FROM AUTHOR]

We present the measurements and modelling of the small-to-intermediate scale (~0.1-25 h-1 Mpc) projected and three-dimensional redshift-space two-point correlation functions (2PCFs) of local galaxies in the Sloan Digital Sky Survey Data Release 7. We find a clear dependence of galaxy clustering on luminosity in both projected and redshift spaces, generally being stronger for more luminous samples. The measurements are successfully interpreted within the halo occupation distribution (HOD) framework with central and satellite velocity bias parameters to describe galaxy kinematics inside haloes and to model redshift-space distortion effects. In agreement with previous studies, we find that more luminous galaxies reside in more massive haloes. Including the redshift-space 2PCFs helps tighten the HOD constraints. Moreover, we find that luminous central galaxies are not at rest at the halo centres, with the velocity dispersion about 30 per cent that of the dark matter. Such a relative motion may reflect the consequence of galaxy and halo mergers, and we find that central galaxies in lower mass haloes tend to be more relaxed with respect to their host haloes. The motion of satellite galaxies in luminous samples is consistent with their following that of the dark matter. For faint samples, satellites tends to have slower motion, with velocity dispersion inside haloes about 85 per cent that of the dark matter. We discuss possible applications of the velocity bias constraints on studying galaxy evolution and cosmology. In the appendix, we characterize the distribution of galaxy redshift measurement errors, which is well described by a Gaussian-convolved double exponential distribution. [ABSTRACT FROM AUTHOR]

We present the measurements of the redshift-space three-point correlation function (3PCF) for z ~ 0.5 luminous red galaxies of the CMASS sample in the Sloan Digital Sky Survey- III Baryon Oscillation Spectroscopic Survey Data Release 11. The 3PCF measurements are interpreted within the halo occupation distribution framework using high-resolution N-body simulations, and the model successfully reproduces the 3PCF on scales larger than 1 h-1 Mpc. As with the case for the redshift-space two-point correlation functions, we find that the redshiftspace 3PCF measurements also favour the inclusion of galaxy velocity bias in the model. In particular, the central galaxy in a halo is on average in motion with respect to the core of the halo. We discuss the potential of the small-scale 3PCF to tighten the constraints on the relation between galaxies and dark matter haloes and on the phase-space distribution of galaxies. [ABSTRACT FROM AUTHOR]

Plants exhibit reduced root growth when exposed to low temperature; however, how low temperature modulates root growth remains to be understood. Our study demonstrated that low temperature reduces both meristem size and cell number, repressing the division potential of meristematic cells by reducing auxin accumulation, possibly through the repressed expression of PIN1/3/7 and auxin biosynthesis- related genes, although the experiments with exogenous auxin application also suggest the involvement of other factor(s). In addition, we verified that ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) and ARR12 are involved in low temperature-mediated inhibition of root growth by showing that the roots of arr1-3 arr12-1 seedlings were less sensitive than wild-type roots to low temperature, in terms of changes in root length and meristem cell number. Furthermore, low temperature reduced the levels of PIN1/3 transcripts and the auxin level to a lesser extent in arr1-3 arr12-1 roots than in wild-type roots, suggesting that cytokinin signaling is involved in the low-temperaturemediated reduction of auxin accumulation. Taken together, our data suggest that low temperature inhibits root growth by reducing auxin accumulation via ARR1/12. [ABSTRACT FROM AUTHOR]

The author discusses the health effects of haze and particulate matters (PM) pollution.